The CIA and the Obama Administration continue to keep secret some of the most shocking allegations involving the spy agency's interrogation program: three deaths and several other detainees whose whereabouts could not be determined, according to a former senior intelligence official who has read the full, unredacted version.

Of the 109 pages in the 2004 report, 36 were completely blacked out in the version made public Monday, and another 30 were substantially redacted for "national security" reasons.

The blacked-out portions hide the Inspector General's findings on the circumstances that led to the deaths of at least three of the detainees in the CIA's program, the official said. Two of the men reportedly died in CIA in Iraq and the third died in Afghanistan.

The Inspector General's findings about a fourth death involving a prisoner in Afghanistan were made public in the report. A CIA contract employee was convicted of assault in that case and is now in prison.

The still-secret portions of the Inspector General's report also describe fears that the waterboarding of 9/11 mastermind Khalid Sheik Mohammed came close to killing him. Mohammed was waterboarded 183 separate times, according to the report.

The unredacted version of the report makes a reference to the "unsafe" nature of waterboarding but makes no mention of its actual effects on Mohammed or the two others who were subjected to the technique.

The ranking Republican on the House Intelligence Committee, Rep. Pete Hoekstra (R-MI), said he thinks more of the CIA's blacked out information should be made public. "If the sections of the report don't talk about sources and methods, at this point in time, my bias would be toward transparency and toward releasing more information." Hoekstra, who has read the unredacted version of the CIA report, said he could not comment on its contents.

Also hidden from public scrutiny, according to the official, was the discovery by the CIA Inspector General that the CIA could not adequately account for several of the 100 al Qaeda suspects who were part of the detainee program that the CIA maintained had been well administered.

The official said "a few just got lost and the CIA does to know what happened to them."

Other detainees, said the official, were transferred to other countries and their whereabouts are still unknown. In other cases, "incomplete records" were to blame for the failure to account for the detainees' status after leaving the program.

Missing Detainees

CIA spokesman Paul Gimigliano told ABC News, "The CIA will cooperate with the Department of Justice, as it always has, in this latest look at past detention and interrogation practices. As the agency has noted previously, career prosecutors at Justice have already examined these cases. That includes, in addition to the complete Inspector General's report—which Justice has had since 2004—other allegations of abuse, which the CIA itself referred to the Department."

In his conclusions, Inspector General John Helgerson, found "the Agency—especially in the early months of the program—failed to provide adequate staffing, guidance and support to those involved with the detention and interrogation of detainees."

Helgerson, who left the job in Mar. 2009, said in a statement, "the primary common problem was that management controls and operational procedures were not in place to avoid the serious problems that arose, jeopardizing Agency employees and detainees alike."

Even after the report was completed in 2004, the problem of missing detainees continued, according to the former intelligence official.

One of the detainees who was put in the "missing" category was identified by the CIA as a top al Qaeda figure, Hassan Ghul, who officials had planned to waterboard until they determined he was "obese" and might lead to serious medical issues.

Ghul was turned over to Pakistan in 2006 and has since been released. The CIA does not know whether he returned to fight with al Qaeda or simply disappeared from sight.

"The primary, common problem was that management controls and operational procedures were not in place to avoid the serious problems that arose," said Helgerson, who served as CIA inspector general from 2002 to Mar. 2009.